AlexanderPico
commented
3 years ago Great notes! The old doc page was outdated and redundant with Swagger. I've replaced it with just a couple links. The GMT files are generated separately from the other download file types (as far as I understand), so they are not accessible from our webservice. I think that takes care of everthing except...
Your point about the data.wikipathways.org site is precisely correct. That site needs to be replaced ASAP. I've polled the group on Slack and the mailing list for ideas. The only idea I have heard so far is to deposit our monthly release files into FigShare. I like this idea, but we have to workout how to automate it and then replace our current monthly scripts with this new approach. Alternative suggestions?
This probably needs quick ideas about how to fix, and then be split in multiple issues.
When Googling for the web service I found this page: https://www.wikipathways.org/index.php/Help:WikiPathways_Webservice/API That page seems to have outdated information compared to the Swagger pages, and probably should just be replaced by Swagger output. It for instance mentions the option to download "txt" files, which I think we no longer support and the getPathwayAs example seems to be broken. It actually gives different errors for gpml files and gmt files.
The page also links to this page: https://www.wikipathways.org/index.php/Download_Pathways to explain the file formats, where I think that should be this one: https://www.wikipathways.org/index.php/Help:FileFormats
I then tried to download the GMT files directly from this page: http://data.wikipathways.org/current/gmt/ That gives a not secure error since that page is not https. More importantly, that also means that at least my Chrome cannot do the actual download.
According to the Swagger documentation the download page does not support downloading GMT files. Is that intended?